//
// Manta - Structural Variant and Indel Caller
// Copyright (c) 2013-2019 Illumina, Inc.
//
// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program.  If not, see <http://www.gnu.org/licenses/>.
//
//

#include "CheckSVLoci.hpp"
#include "CSLOptions.hpp"

#include "svgraph/SVLocusSet.hpp"

static void runCSL(const CSLOptions& opt)
{
  SVLocusSet set(opt.graphFilename.c_str());
  set.finalize();
  set.checkState(true, true);
}

void CheckSVLoci::runInternal(int argc, char* argv[]) const
{
  CSLOptions opt;

  parseCSLOptions(*this, argc, argv, opt);
  runCSL(opt);
}
